/*
 * JGO2RDF creates a RDF representation of GAF2 files, which are automatically sourced from GO ftp site.
 * Copyright (C) 2012 Matthew M. Hindle & Artem Lysenko
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package uk.co.jgo2rdf.rdf.refseq;

/**
 * @author hindlem
 *         Date: 4/26/11
 *         Time: 11:34 AM
 * @version 0.10
 */
public class URIs {

    public static final String NCBITaxon = "http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=";
    public static String UniProtURI = "http://purl.uniprot.org/uniprot/";


    public static final String NCBI = "http://www.ncbi.nlm.nih.gov/nuccore/";
    public static final String ZFIN = "http://zfin.org/cgi-bin/ZFIN_jump?record=";
    public static final String MGI = "http://www.informatics.jax.org/searches/accession_report.cgi?id=";
    public static final String RGD = "http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=";
    public static final String FLYBASE = "http://fly.ebi.ac.uk:7081/.bin/fbidq.html?";
    public static final String SGD = "http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=";
    public static final String WORMBASE = "http://www.wormbase.org/db/misc/paper?name=";

    public static final String WORMBASE_GENE = "http://www.wormbase.org/db/gene/gene?name=";

    public static final String SOYBASE = "http://soybase.agron.iastate.edu/";
    public static final String RICEGENES = "http://www.gramene.org/";

    public static final String GRAMENE = "http://www.gramene.org/db/genes/search_gene?acc=";
    public static final String TAIR_LOCUS = "http://arabidopsis.org/servlets/TairObject?type=locus&name=";
    public static final String TAIR_ACCESSION = "http://www.arabidopsis.org/servlets/TairObject?accession=";

    public static final String AspGD = "http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=";
    public static final String AspGD_Locus = "http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=";

    public static final String CGD = "http://www.candidagenome.org/cgi-bin/locus.pl?dbid=";
    public static final String CGD_Locus = "http://www.candidagenome.org/cgi-bin/locus.pl?locus=";
    public static final String CGD_Ref = "http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=";

    public static final String DictyBase = "http://dictybase.org/db/cgi-bin/gene_page.pl?dictybaseid=";
    public static final String Lmajor = "http://www.genedb.org/genedb/Search?organism=leish&name=";
    public static final String Pfalciparum = "http://www.genedb.org/genedb/Search?organism=malaria&name=";
    public static final String Spombe = "http://www.genedb.org/genedb/Search?organism=pombe&name=";
    public static final String Tbrucei = "http://www.genedb.org/genedb/Search?organism=tryp&name=";

    public static final String ASAP = "https://asap.ahabs.wisc.edu/asap/";
    public static String SGN = "http://solgenomics.net/locus/%s/view";

    public static final String TIGR_CMR = "http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=";
    public static String VMD = "http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=";

    public static String JVCI_CMR = "http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=";

}
